Avirulence genes identified through linkage mapping and region-specific association studies in the wheat leaf rust pathogen Puccinia triticina

Wheat rust fungi can cause significant damage to wheat crops, leading to reduced yields and economic losses. To combat disease, certain plant varieties can trigger defense responses upon recognition of specific pathogen effector proteins, thereby conferring avirulence. Identifying such avirulence (Avr) genes is crucial for developing strategies to protect crops from devastating losses, ranging from identifying matching resistance genes to designing diagnostic assays for monitoring pathogen populations. Puccinia triticina (Pt) causes wheat leaf rust and is an obligate biotrophic fungus, and because of its life cycle and mode of reproduction, it is difficult to study genetically. To identify Avr genes in Pt, a F2 population of fifty-seven progeny was generated from a sexual cross of race 9 (SBDG) and race 161 (FBDJ) on the alternate host Thalictrum speciosissimum under controlled conditions. The population segregated for avirulent/virulent traits screened at the seedling stage on thirteen single gene resistance lines in the wheat host cultivar Thatcher background. The genomes of the parents, F1, and progeny were sequenced and mapped onto an assembled parental race 9 phased haplotype B genome, resulting in the generation of 21,154 high-quality SNP markers suitable for genetic mapping of the F2 population. A genetic map composed of 61 linkage groups was obtained, containing a total of 10,923 markers, and spanning 10,730.5 centimorgans. Effector loci correlating with avirulence to specific leaf rust resistance (Lr) genes, PtAvrLr14a, PtAvrLr11 and PtAvrLr2a, were mapped to chromosome 1, chromosome 3 and chromosome 4, respectively. To strengthen the identification of candidate Avr genes, a region-specific association study was done on a natural population of fifty-nine Pt isolates that were collected in Canada and whose genomes were sequenced using Illumina. Significant markers and corresponding candidate effector genes were identified for these mapped Avr loci. The identification of these candidate genes is an essential step towards cloning Avr and subsequentially their matching host resistance genes, and for studying the molecular mechanisms underlying pathogen-host interactions and host defense.